Contacts of the helix formed by residues 400 - 405 (chain D) in PDB entry 2DB3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 400 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D LYS* 6.0 0.5 - - - -
326D PRO* 3.7 21.3 - - + -
330D LEU* 3.7 23.2 - - + +
399D ASP* 1.3 84.6 + - - +
401D ALA* 1.3 66.4 + - - +
402D ASP* 3.3 5.2 - - - -
403D ARG* 3.0 11.5 + - + +
404D MET* 3.2 9.7 + - - +
431D PHE 2.9 11.1 + - - -
432D SER* 4.1 4.5 + - - +
551D ARG* 2.7 48.8 + - + +
552D GLY* 3.3 25.0 + - - -
575D HIS* 3.3 11.4 + - - -
2804D MG 3.9 5.2 - - - -
2904D ANP 3.6 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D LEU* 3.5 23.8 - - + +
399D ASP 2.9 4.5 - - - -
400D GLU* 1.3 77.6 - - - +
402D ASP* 1.3 62.4 + - - +
404D MET* 3.1 3.8 + - - +
405D LEU* 3.1 26.9 + - - +
430D MET* 3.6 30.5 - - + -
431D PHE 2.9 11.6 + - - +
432D SER* 3.9 0.4 - - - -
435D PHE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ALA* 1.3 75.3 - - - +
403D ARG* 1.3 59.8 + - - -
405D LEU 3.5 0.3 + - - -
406D ASP* 3.3 23.2 + - - +
432D SER* 2.6 10.5 + - - -
434D THR* 2.5 40.8 + - - +
435D PHE* 4.0 7.4 - - + -
436D PRO* 3.9 16.4 - - + +
439D ILE* 3.6 31.3 - - + +
551D ARG* 2.5 30.3 + - - -
571D ASP* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D PRO* 3.9 21.3 - - + -
400D GLU* 3.0 12.4 + - + +
402D ASP* 1.3 83.3 + - - +
404D MET* 1.3 61.8 + - - +
405D LEU 3.3 0.7 + - - -
406D ASP* 3.4 29.7 + - - +
408D GLY* 5.9 6.0 - - - -
409D PHE* 3.7 20.7 + - + +
551D ARG* 3.6 37.0 - - - +
569D LYS* 5.5 9.3 - - - +
2H U 5.7 1.0 + - - +
3H U 2.8 33.1 + - - +
4H U 4.9 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D VAL* 3.2 33.9 - - + +
325D SER 3.7 5.6 - - - +
326D PRO* 3.2 41.1 - - + -
376D PRO* 3.4 21.5 - - + -
398D LEU* 4.3 13.9 - - + -
399D ASP 3.4 11.7 - - - +
400D GLU 3.4 12.6 - - - +
401D ALA* 3.1 7.0 + - - +
403D ARG* 1.3 76.3 - - - +
405D LEU* 1.3 57.5 + - - +
409D PHE* 3.2 33.7 - - + +
410D SER 3.6 0.3 + - - -
413D MET* 3.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D LEU* 4.1 11.0 - - + -
401D ALA 3.1 18.5 + - - +
402D ASP 3.9 0.7 - - - -
403D ARG 3.2 0.2 - - - -
404D MET* 1.3 76.8 - - - +
406D ASP* 1.3 62.8 + - - +
410D SER* 3.7 15.0 - - - -
413D MET* 4.4 6.1 - - + -
417D MET* 4.1 25.6 - - + -
430D MET* 3.8 12.8 - - + -
435D PHE* 4.5 2.7 - - + -
439D ILE* 3.8 19.1 - - + +
442D MET* 3.4 25.5 - - + +
443D ALA* 3.4 39.3 - - + +
446D PHE* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il